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Vitamin B12 Deficiency: Why Gut Health Matters

Written by Dr. Michael Ruscio, DC on August 20, 2024

Written by Dr. Michael Ruscio, DC on August 20, 2024 — Reviewed by Hannah Wright

How Healing Your Gut Can Help Optimize Your Vitamin B12 Levels

• What is Vitamin B12?|
• Deficiency Signs and Symptoms|
• Am I at Risk?|
• What’s My Vitamin B12 Status?|
• Causes of B12 Deficiency|
• Healing Your Gut|
• Vitamin B12 Supplements|
• Healing Your Gut Improves B12|

Some estimates suggest that up to 43% of adults may not have enough vitamin B12 [1]. Though other estimates are somewhat lower, one thing we can say is that vitamin B12 deficiency is surprisingly common.

Vitamin B12 is critical for your nervous system and blood, so a large drop (deficiency) or even a milder drop (insufficiency) in B12 can cause symptoms like anxiety, depression, dementia (cognitive impairment), peripheral neuropathy (burning or numbness in your limbs), and anemia (pale skin, fatigue, and weakness) [2, 3]. Additionally, inadequate vitamin B12 during pregnancy can spell trouble for both mom and baby [2]. 

It may seem like common sense to think of a B12 deficiency as just a lack of dietary intake, which is often the case for vegans and vegetarians. But for most people who consume a variety of animal foods or take B12 supplements, B12 deficiency is more likely related to poor absorption. 

It’s easy, even for doctors, to overlook vitamin B12 insufficiency or deficiency, so I want to share the early warning signs, the best ways to determine your B12 status, and why targeting your gut health (with diet and probiotics) is so important for maintaining optimal levels of vitamin B12. I’ll also provide clear guidance on supplementation, but before we get into the specifics, let’s start off with a little background on vitamin B12.

What is Vitamin B12?

Your body requires six main nutrients (carbohydrates, protein, fat, vitamins, minerals, and water) to function normally. The B vitamins are a group of eight water-soluble vitamins that your body uses for everything from converting the food you eat into energy and making and repairing DNA, to keeping cells alive and creating neurotransmitters [4]. 

Vitamin B12, also known as cobalamin, is a B vitamin that’s especially important for your blood and nervous system. It helps your body make new blood cells and create DNA, fatty acids, and myelin sheaths (the fatty covering that allows impulses to be sent across your nerve cells) [5, 6]. These are all super-important functions, so if you’re lacking in B12, you can run into some serious health issues. Let’s discuss how a B12 deficiency can make you feel and some of the health consequences that can arise.

Vitamin B12 Deficiency: Signs and Symptoms 

Vitamin B12 insufficiency and deficiency symptoms can exist on a spectrum, so you may not even recognize them at first. But as your B12 level gets lower and lower, symptoms can begin to significantly impact your quality of life. 

Here are the most common signs and symptoms of vitamin B12 deficiency [2, 3]:

• Macrocytic anemia, megaloblastic form (when your red blood cells are too large and they don’t have enough nutrients to function normally) [6].
  • Signs of anemia include:

• Pale skin
• Fatigue
• Weakness
• Feeling cold
• Elevated heart rate
• Dizziness when standing
• Shortness of breath

• Glossitis (inflammation of the tongue that includes pain, redness, swelling, and lesions)
• Peripheral neuropathy (burning, stabbing, stinging, and numbness in the extremities)
• Psychiatric disturbances like anxiety, depression, apathy, memory loss, and dementia
• Additional symptoms like headaches, vision loss, altered reflexes, and abnormal gait (walking pattern)

If the B12 deficiency is caused by an autoimmune condition, such as pernicious anemia or autoimmune atrophic gastritis, you may experience these additional symptoms [7, 8, 9]: 

• Stomach pain and burning
• Nausea
• Vomiting
• Loss of appetite
• Heartburn
• Fullness in the upper abdomen
• Diarrhea
• Iron deficiency
• Hypochlorhydria (low stomach acid)

Vitamin B12 deficiency during pregnancy increases your risk of high blood pressure (preeclampsia), which can lead to other serious health problems in organs like the kidney and liver. But your growing baby can also experience negative effects like [2]: 

• Neural tube defects
• Stunted growth in utero (before birth)
• Low lean mass and excess fat 
• Insulin resistance
• Increased risk of developing a chronic disease
• Reduced or delayed sensory responses

In many cases, the symptoms of a vitamin B12 deficiency come on slowly and may not be noticeable until the deficiency is really obvious. Thus, it’s important to find out if you’re at high risk, and I’ll help you understand how [9].

Vitamin B12 Deficiency: Am I at Risk? 

Anyone can become deficient in vitamin B12, but here are some factors that place you at higher risk [2]:

• Being elderly
• Having Northern European ancestry
• Consuming a primarily plant-based diet
• Having an inflammatory condition in your GI tract, such as inflammatory bowel disease chronic atrophic gastritis, or celiac disease [6]
• Being pregnant
• Having an autoimmune condition, such as Hashimoto’s thyroiditis, rheumatoid arthritis, psoriasis, Sjogren’s disease, type 1 diabetes, or celiac disease) [6, 9]
• Taking certain medications, including Metformin for longer than 4 months, and proton pump inhibitors (PPIs) or H2 receptor antagonists for longer than a year [10]

The risk factors listed here seem to apply to a large swath of people, so you may be wondering how common vitamin B12 deficiency really is.

What’s My Vitamin B12 Status?

Knowing if you have enough vitamin B12 can be somewhat tricky. You might think that simply getting a vitamin B12 blood test would tell you whether or not you have enough of this vitamin. But serum (blood) levels are unreliable and shouldn’t be used by themselves to determine your vitamin B12 status [3]. For a more complete picture, it’s important to run some additional tests.

Here’s a chart of labs that can be helpful [3, 6]:

As you can see, it can take some investigation to determine your total vitamin B12 status, so it’s important to work with a healthcare provider if you’re at high risk and suspect you may have symptoms of deficiency.  

Once you’ve been diagnosed with vitamin B12 deficiency, taking high doses of the vitamin and expecting everything to right itself may not lead to long-term success. If your levels and symptoms don’t improve, it’s extremely important to look for and treat the root cause. Your healthcare provider may recommend the following additional diagnostic labs or tests to uncover why you’re still experiencing a B12 deficiency [6, 9]:

• Intrinsic factor blocking antibodies are reliable indicators of pernicious anemia (an autoimmune condition that prevents you from absorbing B12). These antibodies can boost your serum (blood) B12 level even if your total body level is low, so your provider may order this test when they suspect you are deficient in B12 despite a normal serum B12 level.
• Anti-parietal cell antibodies can indicate autoimmune atrophic gastritis or other autoimmune conditions (but not pernicious anemia), but these antibodies can also be present in healthy people and must be interpreted cautiously.
• Serum gastrin is a hormone that helps with stomach acid production. High levels can indicate you have a B12 deficiency.
• Upper GI endoscopy (with or without a biopsy) can check for H. pylori infection, autoimmunity, and cellular hyperplasia (enlargement of a tissue or organ) or metaplasia (a change from one type of cell to another), which can all accompany chronic or autoimmune atrophic gastritis and low B12 levels. This test, with a biopsy of the small intestine, can also rule out celiac disease, which can contribute to poor B12 absorption.
• Colonoscopy can rule out inflammatory bowel disease (IBD) or other issues in the lower GI tract that could be impacting your ability to absorb vitamin B12.

Now that I’ve gone over the background on vitamin B12, I’d like to share with you the main causes of vitamin B12 deficiency and how I go about treating it in the clinic.  

Common Causes of Vitamin B12 Deficiency

 Vitamin B12 deficiency may be hard to detect and could be going undiagnosed in many people. The National Institutes of Health estimates that between 3% and 43% of older adults in the U.S. are deficient in B12 [1]. 

When considering the causes of a vitamin deficiency, it’s easy to assume that you’re just not eating enough foods containing that vitamin (or other nutrient). But inadequate dietary B12 intake is just one cause, and it’s usually related to a vegan or vegetarian diet. Other common culprits include malabsorption and autoimmunity [6]. Let’s dig into the specifics of each of these reasons your B12 may be low.

Inadequate Dietary B12 Intake 

Animal-based foods like meat, dairy products, and eggs are the major sources of vitamin B12 in the diet. So, this is why vegans and vegetarians have a higher risk of developing an insufficiency or deficiency. One review found that vitamin B12 deficiency may be as high as 87% in vegetarian adults [11].

Vitamin B12 is stored primarily in your liver until your body needs to use it, so if you go from an animal-based to plant-based diet, you’ll still have some B12 available for a while. However, after about 3 years (although this will vary based on the individual), the body completely drains its liver stores of vitamin B12, and deficiency is on the horizon [6]. 

Malabsorption and Vitamin B12

Outside of not consuming enough B12 in your diet, malabsorption can cause you to become deficient. Before we get into specific conditions that lead to malabsorption, I want to explain how and where you absorb vitamin B12.

After you eat foods containing B12, special proteins in your stomach bind to B12 and carry it to the small intestine to be absorbed. But first, it must bind to a protein called intrinsic factor (IF). IF is pivotal in B12 absorption—without it, even if you are eating B12-rich foods, your small intestine can’t absorb it. 

A number of digestive system imbalances can prevent the absorption of any nutrient, including B12, whether it’s in food or supplements. For example, having too little or too much stomach acid, microbial dysbiosis (imbalance in gut microbes), or a leaky gut can lead to malabsorption [12, 13, 14, 15]. 

Conditions that cause inflammation in the small intestine can also inhibit absorption and lead to a B12 deficiency; these include [2, 3, 6]:

• Inflammatory bowel disease (Crohn’s disease)
• Bowel resections (partial or complete removal of the small or large intestine)
• Gastric bypass surgery
• Celiac disease
• Intestinal pathogens and small intestinal bacterial overgrowth (SIBO)

And if that’s not enough, exocrine pancreatic insufficiency (when your pancreas can’t make enough enzymes to break down your food) and long-term use of common medications, including Metformin and PPIs, can prevent vitamin B12 absorption [10, 16, 17]. 

Autoimmunity, Intrinsic Factor, and Vitamin B12

Although the next two conditions do impact absorption, they do it in a very specific way, even before absorption begins. Pernicious anemia is an autoimmune condition that both attacks cells lining the inside of the stomach and blocks intrinsic factor. In similar fashion, the anti-parietal cell antibodies related to autoimmune gastritis can prevent the stomach’s parietal cells from making IF. Both of these autoimmune attacks leave incoming B12 high and dry, unavailable for the small intestine to absorb [6].

To sum this up, vitamin B12 deficiency is most often due to insufficient dietary intake, a gut issue that’s causing malabsorption, or autoimmunity that prevents B12 from being readied for absorption. What this tells me is that simply adding a vitamin B12 supplement won’t resolve the underlying issue in all cases. 

In patients whose vitamin B12 is too low simply because they’re not eating enough sources of it, implementing a nutrient-dense diet and taking B12 supplements as needed may be enough to bring their vitamin B12 levels back to normal for good.

But when the root cause of cobalamin deficiency is gut related or autoimmune in nature, it’s important to start a gut-directed treatment, including a nutrient-dense anti-inflammatory diet and probiotics, to move the B12 needle in the right direction and keep it at optimal levels. At the clinic, we’ve found it’s best to address gut health and absorption issues before trying to optimize nutrient levels, so let’s get into some effective ways to heal your gut.

Healing Your Gut With Diet and Probiotics

Since malabsorption is often a root cause of vitamin B12 deficiency, it makes sense to find the cause of malabsorption before loading you up with mega-doses of supplemental vitamins. Think about it this way: optimal gut function translates into optimal absorption of nutrients (including vitamin B12). So, how can you heal your gut? In my experience, dietary changes are among the most powerful tools we have for healing the gut, reducing autoimmunity, and improving your overall health, so I like to start there first. 

Gut Healing Diet Options

It’s true: dietary advice can be confusing. But it might help you wrap your head around it if you know that my major goals for using diet therapy to heal your gut include:

• Reducing your exposure to food allergens and intolerances
• Providing your gut microbiome with the fuel it needs
• Promoting better blood sugar control
• Focusing on fresh, whole, unprocessed foods

As you’ll find in my book, Healthy Gut, Healthy You, many different dietary plans fit these criteria. But as a general rule, it’s best to start with the least restrictive diet, moving on to a more specialized protocol only if your symptoms don’t improve enough. 

So, if you’re following a pretty standard American diet, then you may want to move to an anti-inflammatory meal pattern like the Mediterranean diet first. This can be a great option if you’re new to making diet-related changes. 

However, if you’re already eating wholesome foods and still struggling with vitamin B12 deficiency or other symptoms of poor gut health, you might consider the Paleo diet, which takes it a step further and removes potential allergens and other gut-disrupting foods. If you trial both of these dietary plans but still need to simplify more, the low FODMAP diet or the autoimmune protocol diet may get you where you need to be. 

While you’re working on finding the right gut-healing diet for you, I recommend a therapeutic trial of probiotics. Now I’ll get into how and why probiotics can improve your vitamin B12 status.

Probiotics Improve Nutrient Absorption

Probiotics are microbes that impart health benefits when we eat them. A small amount of research suggests that probiotics may specifically improve vitamin B12 absorption. A 2021 systematic review of 14 clinical trials found that when healthy people of all ages took probiotics, they had higher levels of not only cobalamin (vitamin B12) but also folic acid (vitamin B9), calcium, iron, and zinc than people who didn’t take probiotics [18].

Literature reviews have found that, in addition to promoting the absorption of various vitamins and minerals, probiotics might also manufacture certain B vitamins, including B1, B2, B3, B6, B8, B9, and B12 [19]. These B vitamins may help prevent malnutrition, provide antioxidants, and reduce inflammation, all of which may promote gut healing [20].

We need more evidence to say that probiotics reliably increase vitamin B12 levels. Fortunately, we have plenty of high-quality research showing that probiotics can help repair underlying gut conditions (like leaky gut, gastritis, SIBO, IBD, and celiac disease) that disrupt your ability to properly absorb nutrients [21, 22, 23].

Probiotics may also help resolve symptoms that you may have associated with B12 deficiency but didn’t improve when you started B12 supplements. Many of these negative symptoms could actually be the result of an unhealthy gut. 

After you’ve started healing your gut with diet and probiotics, you’ll likely need to consider vitamin B12 supplementation, but what’s the best option? You may have heard that injections are better than supplements you take by mouth, so let’s look at the research.

Vitamin B12 Supplementation

I typically prefer to heal the gut before trying to optimize nutrient levels. That said, it’s important to avoid possible negative consequences of a vitamin B12 deficiency, such as permanent neurological damage, anemia, or danger during pregnancy. Since there’s no known risk to taking too much vitamin B12, it makes sense to take supplemental B12 while you’re working on addressing the underlying causes with a nutrient-dense diet and gut-healing strategies [2]. Now the question is, which kind should you take?

Correcting Your Vitamin B12 Level With Supplements 

Vitamin B12 supplements come in various forms, including cyanocobalamin (most common), methylcobalamin, hydroxocobalamin, and adenosylcobalamin. Cyanocobalamin gets its name from the cyanide group attached to it, and it’s the only form that’s not found naturally in the body [24]. While all forms seem to have equal absorption rates and effectively increase serum (blood) levels, the body may excrete more cyanocobalamin than the others. On top of that, cyanocobalamin isn’t stored as easily in the liver or other tissues, all of which means it’s probably less bioavailable compared to the other forms. Additionally, there might be a safety issue concerning the buildup of cyanide in the tissues [24].

When it comes to using supplements, oral, sublingual (under the tongue), and intramuscular injections (shots into the muscle) are all great for correcting an insufficient or deficient B12 level. The standard dose is 1,000–2,000 micrograms per day [10, 25, 26]. If you have severe symptoms of B12 deficiency, or you’re pregnant or lactating, you may want to speak with your healthcare provider about intramuscular injections, as they’re more fast acting [10].

Maintaining Your Vitamin B12 Level

Once your vitamin B12 level is back in normal range (greater than 300 pg/mL), a nutrient-dense diet should be enough to maintain your B12 if the deficiency was simply related to a lack of dietary intake [27, 28, 29, 30]. Here’s a list of foods that are high in vitamin B12 [31]:

• Beef and beef liver
• Fortified nutritional yeast
• Clams, salmon, and tuna
• Milk, yogurt, and cheese
• Fortified cereals
• Eggs
• Turkey

As you can see, the majority of these are animal-based foods, so if you follow a vegan or vegetarian diet, you probably need vitamin B12 supplements to maintain healthy levels [10]. If you’re getting B12 injections, once your level is optimal, you can probably decrease the frequency to 1–4 times a month, or as needed [26]. If you’re taking oral B12, then you may want to take 500–1,000 mcg per day for maintenance. In either case, it’s best to check this out with your doctor first and track your levels together regularly [25].

If your B12 level is low due to an underlying cause like poor gut health or having used certain medications (like Metformin or acid blockers) for a long time, you’ll want to continue with vitamin B12 supplements to maintain your level while you’re working to correct the root cause(s). 

Of course, ignoring the root cause(s) and relying completely on B12 injections or supplements to maintain your B12 levels isn’t the best option. Nevertheless, when it comes to vitamin B12, it’s best to err on the side of caution. But is it possible to take too much vitamin B12?

Vitamin B12: Can You Take Too Much?

Vitamin B12 supplements are considered safe, and there’s no known upper (toxic) limit. However, research doesn’t support the use of supplemental vitamin B12 in healthy people who have non-specific symptoms like fatigue or cognitive decline without clear indications of a B12 deficiency. The concern here is that you might attribute your symptoms to B12 deficiency when something else (like poor gut health) is causing them. If you take B12 unnecessarily without finding the true root cause, you might waste your money while not getting closer to healing. But you’re not likely to experience any adverse effects of B12 supplements.

Heal Your Gut To Improve Your B12 Level 

Vitamin B12 deficiency is likely common and most often results from low dietary intake, malabsorption from poor gut health, or certain autoimmune diseases. Inadequate vitamin B12 levels can lead to serious health consequences like anemia, poor cognitive function, numbness in the extremities, vision loss, and negative pregnancy outcomes.  

Determining your vitamin B12 status can be somewhat challenging and may require several different tests. Once you’ve been diagnosed with a vitamin B12 deficiency, it’s best to replenish your levels with supplements while you work to identify and treat root causes like inadequate diet, poor gut health, or autoimmunity.

An anti-inflammatory, nutrient-dense diet and probiotics are well-supported interventions for healing your gut, which can reduce inflammation and autoimmunity, improving your ability to absorb all dietary nutrients, including vitamin B12. If you suspect poor gut health is impacting your nutritional status, you may want to work through the Great-In-8 action plan for healing your gut, outlined in Healthy Gut, Healthy You. If you’d like more personalized guidance, contact us at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.